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Replication initiator protein REPE54 and cognate DNA sequence with terminal three prime phosphates.
Analyse Replication initiator protein REPE54 and cognate DNA sequence with terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SDP
- Type
- protein + DNA
- Length
- 274 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*A)- 3'); DNA…
- UniProt
- Q0E856
- Ligands
- MG
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*A)- 3') | dna | 21 | — | — |
| B | DNA (5'- D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*A)- 3') | dna | 21 | — | — |
| C | Repb family plasmid replication initiator protein | protein | 225 | 40% helix, 28% strand | Q0E856 |
| F | Unknown polymer fragment | protein | 3 | 0% helix, 0% strand | — |
| D | Unknown polymer fragment | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.62 | 0.78 | 41 | MG |
| 2 | 58 | 0.39 | 0.81 | 15 | empty |
| 3 | 51 | 0.26 | 0.73 | 14 | empty |
| 4 | 52 | 0.25 | 0.73 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 952 Ų buried · 89 hydrogen bonds · nucleic-nucleic
- B–C · 886 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 652 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–F · 190 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 187 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7SDP · Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q0E856
- Elsewhere: RCSB PDB 7SDP · PDBe 7SDP · UniProt Q0E856
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